scholarly journals Comparative and population genomics approaches reveal the basis of adaptation to deserts in a small rodent

2019 ◽  
Author(s):  
Anna Tigano ◽  
Jocelyn P. Colella ◽  
Matthew D. MacManes
Keyword(s):  
North America ◽  
Population Genomics ◽  
Protein Denaturation ◽  
Gene Families ◽  
Small Rodent ◽  
Selective Sweeps ◽  
Cellular Mechanisms ◽  
Dietary Shift ◽  
Recent Emergence ◽  
Signature Of Selection

AbstractOrganisms that live in deserts offer the opportunity to investigate how species adapt to environmental conditions that are lethal to most plants and animals. In the hot deserts of North America, high temperatures and lack of water are conspicuous challenges for organisms living there. The cactus mouse (Peromyscus eremicus) displays several adaptations to these conditions, including low metabolic rate, heat tolerance, and the ability to maintain homeostasis under extreme dehydration. To investigate the genomic basis of desert adaptation in cactus mice, we built a chromosome-level genome assembly and resequenced 26 additional cactus mouse genomes from two locations in southern California (USA). Using these data, we integrated comparative, population, and functional genomic approaches. We identified 16 gene families exhibiting significant contractions or expansions in the cactus mouse compared to 17 other Myodontine rodent genomes, and found 232 sites across the genome associated with selective sweeps. Functional annotations of candidate gene families and selective sweeps revealed a pervasive signature of selection at genes involved in the synthesis and degradation of proteins, consistent with the evolution of cellular mechanisms to cope with protein denaturation caused by thermal and hyperosmotic stress. Other strong candidate genes included receptors for bitter taste, suggesting a dietary shift towards chemically defended desert plants and insects, and a growth factor involved in lipid metabolism, potentially involved in prevention of dehydration. Understanding how species adapted to the recent emergence of deserts in North America will provide an important foundation for predicting future evolutionary responses to increasing temperatures, droughts and desertification in the cactus mouse and other species.

scholarly journals Fine-mapping the Favored Mutation in a Positive Selective Sweep

2017 ◽  
Author(s):  
Ali Akbari ◽  
Joseph J. Vitti ◽  
Arya Iranmehr ◽  
Mehrdad Bakhtiari ◽  
Pardis C. Sabeti ◽  
...  
Keyword(s):  
Selective Sweep ◽  
Population Genomics ◽  
Simulated Data ◽  
Human Populations ◽  
Selective Sweeps ◽  
1000 Genomes ◽  
Candidate Mutation ◽  
African Populations ◽  
Signature Of Selection ◽  
Out Of Africa

AbstractMethods to identify signatures of selective sweeps in population genomics data have been actively developed, but mostly do not identify the specific mutation favored by the selective sweep. We present a method, iSAFE, that uses a statistic derived solely from population genetics signals to pinpoint the favored mutation even when the signature of selection extends to 5Mbp. iSAFE was tested extensively on simulated data and in human populations from the 1000 Genomes Project, at 22 loci with previously characterized selective sweeps. For 14 of the 22 loci, iSAFE ranked the previously characterized candidate mutation among the 13 highest scoring (out of ∼ 21, 000 variants). Three loci did not show a strong signal. For the remaining loci, iSAFE identified previously unreported mutations as being favored. In these regions, all of which involve pigmentation related genes, iSAFE identified identical selected mutations in multiple non-African populations suggesting an out-of-Africa onset of selection. The iSAFE software can be downloaded from https://github.com/alek0991/iSAFE.

scholarly journals Population genomics of Vibrionaceae isolated from an endangered oasis reveals local adaptation after an environmental perturbation.

2019 ◽  
Author(s):  
Valeria Souza ◽  
Mirna Vazquez-Rosas-Landa ◽  
Gabriel Yaxal Ponce-Soto ◽  
Jonás A. Aguirre-Liguori ◽  
Shalabh Thakur ◽  
...  
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Local Adaptation ◽  
Population Genomics ◽  
Gene Families ◽  
Effective Population ◽  
Pan Genome ◽  
Rare Biosphere ◽  
Recent Origin ◽  
Cuatro Ciénegas Basin

Abstract Background In bacteria, pan-genomes are the result of the evolutionary "tug of war" between selection and horizontal gene transfer (HGT). High rates of HGT increase the genetic pool and the effective population size, resulting in open pan-genomes. In contrast, selective pressures can lead to local adaptation by purging the variation introduced by HGT, resulting in closed pan-genomes and clonal lineages. In this study, we explored both hypotheses elucidating the pan-genome of Vibrionaceae isolates after a perturbation event in the endangered oasis of Cuatro Ciénegas Basin (CCB), Mexico, and looking for signals of adaptation to the environments in their genomes.Results We obtained 42 genomes of Vibrionaceae distributed in six lineages, two of them did not showed any close reference strain in databases. Five of the lineages showed closed pan-genomes and were associated to either water or sediment environment; their high effective population size ( N e ) estimates suggest that these lineages are not from a recent origin. The only clade with an open pan-genome was found in both environments and was formed by ten genetic groups with low N e , suggesting a recent origin. The recombination and mutation estimators (r/m) ranged from 0.0052 to 2.7249, which are similar to oceanic Vibrionaceae estimations; however, we identified 367 gene families with signals of positive selection, most of them found in the core genome; suggesting that despite recombination, natural selection moves the Vibrionaceae CCB lineages to local adaptation purging the genomes and keeping closed pan-genome patterns. Moreover, we identify 598 SNPs associated with an unstructured environment; some of the genes under this SNPs were related to sodium transport.Conclusions Different lines of evidence suggest that the sampled Vibrionaceae, are part of the rare biosphere usually living under famine conditions. Two of these lineages were reported for the first time. Most Vibrionaceae lineages of CCB are adapted to their microhabitats rather than to the sampled environments. This pattern of adaptation is concordant with the association of closed pan-genomes and local adaptation.

scholarly journals From Pavement to Population Genomics: Characterizing a Long-Established Non-native Ant in North America Through Citizen Science and ddRADseq

2019 ◽  
Vol 7 ◽  
Author(s):  
Yuanmeng Miles Zhang ◽  
Tyler R. Vitone ◽  
Caroline G. Storer ◽  
Adam C. Payton ◽  
Robert R. Dunn ◽  
...  
Keyword(s):  
North America ◽  
Citizen Science ◽  
Population Genomics

scholarly journals Reference transcriptomes and comparative analyses of six species in the threatened rosewood genus Dalbergia

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Tin Hang Hung ◽  
Thea So ◽  
Syneath Sreng ◽  
Bansa Thammavong ◽  
Chaloun Boounithiphonh ◽  
...  
Keyword(s):  
Population Genomics ◽  
Association Studies ◽  
Divergence Time ◽  
Gene Families ◽  
Resistance Proteins ◽  
Gene Environment ◽  
International Attention ◽  
Phylogenomic Analyses ◽  
Unique Genes ◽  
Future Population

Abstract Dalbergia is a pantropical genus with more than 250 species, many of which are highly threatened due to overexploitation for their rosewood timber, along with general deforestation. Many Dalbergia species have received international attention for conservation, but the lack of genomic resources for Dalbergia hinders evolutionary studies and conservation applications, which are important for adaptive management. This study produced the first reference transcriptomes for 6 Dalbergia species with different geographical origins and predicted ~ 32 to 49 K unique genes. We showed the utility of these transcriptomes by phylogenomic analyses with other Fabaceae species, estimating the divergence time of extant Dalbergia species to ~ 14.78 MYA. We detected over-representation in 13 Pfam terms including HSP, ALDH and ubiquitin families in Dalbergia. We also compared the gene families of geographically co-occurring D. cochinchinensis and D. oliveri and observed that more genes underwent positive selection and there were more diverged disease resistance proteins in the more widely distributed D. oliveri, consistent with reports that it occupies a wider ecological niche and has higher genetic diversity. We anticipate that the reference transcriptomes will facilitate future population genomics and gene-environment association studies on Dalbergia, as well as contributing to the genomic database where plants, particularly threatened ones, are currently underrepresented.

scholarly journals Population genomics of two closely related anhydrobiotic midges reveals differences in adaptation to extreme desiccation

2020 ◽  
Author(s):  
N.M. Shaykhutdinov ◽  
G.V. Klink ◽  
S.K. Garushyants ◽  
O.S. Kozlova ◽  
A.V. Cherkasov ◽  
...  
Keyword(s):  
Population Genomics ◽  
Expression Profiles ◽  
Gene Families ◽  
Genomic Region ◽  
Ancestral Gene ◽  
New Genes ◽  
Protective Genes ◽  
Duplication Events ◽  
Polypedilum Vanderplanki ◽  
The Sleeping Chironomid

AbstractThe sleeping chironomid Polypedilum vanderplanki is capable of anhydrobiosis, a striking example of adaptation to extreme desiccation. Tolerance to complete desiccation in this species is associated with the emergence of multiple paralogs of protective genes. One of the gene families highly expressed under anhydrobiosis and involved in this process are protein-L-isoaspartate (D-aspartate) O-methyltransferases (PIMTs). Recently, a closely related anhydrobiotic midge from Malawi, P. pembai, showing the ability to tolerate complete desiccation similar to that of P. vanderplanki, but experiences more frequent desiccation-rehydration cycles due to differences in ecology, was discovered. Here, we sequenced and assembled the genome of P. pembai and performed a population genomics analysis of several populations of P. vanderplanki and a population of P. pembai. We observe positive selection and radical changes in the genetic architecture of the PIMT locus between the two species, including multiple duplication events in the P. pembai lineage. In particular, PIMT-4, the most highly expressed of these PIMTs, is present in six copies in the P. pembai; these copies differ in expression profiles, suggesting possible sub- or neofunctionalization. The nucleotide diversity (π) of the genomic region carrying these new genes is decreased in P. pembai, but not in the orthologous region carrying the ancestral gene in P. vanderplanki, providing evidence for a selective sweep associated with post-duplication adaptation in the former. Overall, our results suggest an extensive recent and likely ongoing, adaptation of the mechanisms of anhydrobiosis.

scholarly journals Novel phylogenetic methods are needed for understanding gene function in the era of mega-scale genome sequencing

2020 ◽  
Vol 48 (5) ◽  
pp. 2209-2219 ◽  
Author(s):  
László G Nagy ◽  
Zsolt Merényi ◽  
Botond Hegedüs ◽  
Balázs Bálint
Keyword(s):  
Genome Sequencing ◽  
Large Scale ◽  
Population Genomics ◽  
Gene Families ◽  
Evolutionary Genomics ◽  
Dark Side ◽  
Full Potential ◽  
The Past ◽  
Phylogenetic Methods ◽  
The Universe

Abstract Ongoing large-scale genome sequencing projects are forecasting a data deluge that will almost certainly overwhelm current analytical capabilities of evolutionary genomics. In contrast to population genomics, there are no standardized methods in evolutionary genomics for extracting evolutionary and functional (e.g. gene-trait association) signal from genomic data. Here, we examine how current practices of multi-species comparative genomics perform in this aspect and point out that many genomic datasets are under-utilized due to the lack of powerful methodologies. As a result, many current analyses emphasize gene families for which some functional data is already available, resulting in a growing gap between functionally well-characterized genes/organisms and the universe of unknowns. This leaves unknown genes on the ‘dark side’ of genomes, a problem that will not be mitigated by sequencing more and more genomes, unless we develop tools to infer functional hypotheses for unknown genes in a systematic manner. We provide an inventory of recently developed methods capable of predicting gene-gene and gene-trait associations based on comparative data, then argue that realizing the full potential of whole genome datasets requires the integration of phylogenetic comparative methods into genomics, a rich but underutilized toolbox for looking into the past.

scholarly journals Cryptococcus gattii: Emergence in Western North America: Exploitation of a Novel Ecological Niche

2009 ◽  
Vol 2009 ◽  
pp. 1-8 ◽  
Author(s):  
Kausik Datta ◽  
Karen H. Bartlett ◽  
Kieren A. Marr
Keyword(s):  
North America ◽  
Pacific Northwest ◽  
Ecological Niche ◽  
Ecological Niche Modeling ◽  
Cryptococcus Gattii ◽  
Host Susceptibility ◽  
Emerging Pathogens ◽  
Animal Populations ◽  
The Pacific ◽  
Recent Emergence

The relatively uncommon fungal pathogenCryptococcus gattiirecently emerged as a significant cause of cryptococcal disease in human and animals in the Pacific Northwest of North America. Although genetic studies indicated its possible presence in the Pacific Northwest for more than 30 years,C. gattiias an etiological agent was largely unknown in this region prior to 1999. The recent emergence may have been encouraged by changing conditions of climate or land use and/or host susceptibility, and predictive ecological niche modeling indicates a potentially wider spread.C. gattiican survive wide climatic variations and colonize the environment in tropical, subtropical, temperate, and dry climates. Long-term climate changes, such as the significantly elevated global temperature in the last 100 years, influence patterns of disease among plants and animals and create niche microclimates habitable by emerging pathogens.C. gattiimay have exploited such a hitherto unrecognized but clement environment in the Pacific Northwest to provide a wider exposure and risk of infection to human and animal populations.

scholarly journals Is Xylella fastidiosa a serious threat to European forests?

2020 ◽  
Author(s):  
Marie-Laure Desprez-Loustau ◽  
Yilmaz Balci ◽  
Daniele Cornara ◽  
Paolo Gonthier ◽  
Cécile Robin ◽  
...  
Keyword(s):  
North America ◽  
Disease Risk ◽  
Climatic Factors ◽  
Xylella Fastidiosa ◽  
Fruit Trees ◽  
Forest Tree ◽  
Forest Trees ◽  
Vector Ecology ◽  
European Forests ◽  
Recent Emergence

Abstract The recent emergence of Olive Quick Decline Syndrome in Italy, caused by Xylella fastidiosa, has drawn attention to the risks posed by this vector-borne bacterium to important crops in Europe (especially fruit trees and grapevine). Comparatively very little is known on actual and potential impacts of this pathogen in forests, in the native (North American) and introduced (European) regions, respectively. The present review aims to address important questions related to the threat posed by X. fastidiosa to European forests, such as the following: What are the symptoms, hosts and impact of bacterial leaf scorch caused by X. fastidiosa on trees in North America? Which forest tree species have been found infected in the introduction area in Europe? How does X. fastidiosa cause disease in susceptible hosts? Are there any X. fastidiosa genotypes (subspecies and sequence types) specifically associated with forest trees? How is X. fastidiosa transmitted? What are the known and potential vectors for forest trees? How does vector ecology affect disease? Is the distribution of X. fastidiosa, especially the strains associated with trees, restricted by climatic factors? Is disease risk for trees different in forest ecosystems as compared with urban settings? We conclude by pointing to important knowledge gaps related to all these questions and strongly advocate for more research about the Xylella-forest pathosystems, in both North America and Europe.

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